My program receives FITS file from INDI server. I need functionality to open FITS files directly from memory without writing to disk. Is this possible for cfitsio and rust-fitsio?

Hi! Thank you so much for your work on this crate - it's been incredibly useful for me.

I have some fits files that store data using the BIT type in a BINTABLE extension. With a one-line change, I was able to unpack the contents into a Vec<u32> just fine. I don't know the ramifications of this change, so please feel free to consult me on this.

An example file is shared below:

https://drive.google.com/file/d/1JTYEQD2f42HZMb7D3wskSx6Wkto3HsVO/view?usp=sharing

Thanks again for your time and effort!

Hey @mindriot101, hope you're doing well. This commit looks rather scary, but that's just because it includes all the cfitsio source code. Feel free to review this if you like and have the time.

One potential point for apprehension here is that the code is not tested under OSX. At my work, we recently got a Mac-using developer, so they can test my commit before it gets merged, should you not want to or have time.

Cheers!

Hi,

could you please look at why NASA files cannot be read using the function? image_data is contains only 0

let filename = "./testdata/UITfuv2582gc.fits";
let mut fptr = fitsio::FitsFile::open(filename).unwrap();
fptr.pretty_print();

let hdu = fptr.hdu(0).unwrap();

let image_data: Vec<f32> = hdu.read_image(&mut fptr, ).unwrap();

Data: https://fits.gsfc.nasa.gov/samples/UITfuv2582gc.fits

Is there any way to save a u16 Vec to a fits file? Currently it says u16 is not implemented for the WriteImage trait when I try to use hdu.write_image for a u16 vector, but can that be added here, or is there a way to change that? I am currently recasting the vector to a u32, but the vector contains 61 million entries, and recasting takes a long time.

I'm trying this:

use fitsio::{*, images::*};

fn main() {
    _ = std::fs::remove_file(r"testfile.fit");

    let mut fptr = FitsFile::create(r"testfile.fit").open().unwrap();

    let description = ImageDescription {
        data_type: ImageType::Float,
        dimensions: &[3, 42, 42],
    };
    let data_to_write = vec![1.0_f32; 3 * 42 * 42];

    let hdu = fptr.create_image("EXTNAME".to_string(), &description).unwrap();

    hdu.write_image(&mut fptr, &data_to_write).unwrap();
}

File is being created but many programs can't read it

rust-fitsio uses ffgiet to determine the dtype of an image HDU. I have an image for which ffgiet returns 20, which runs me into an unreachable!(). The cfitsio docs suggest this shouldn't be possible. The header starts off like this:

SIMPLE  =                    T                                                  
BITPIX  =                   16 /8 unsigned int, 16 & 32 int, -32 & -64 real     
NAXIS   =                    2 /number of axes                                  
NAXIS1  =                 1024 /fastest changing axis                           
NAXIS2  =                 1024 /next to fastest changing axis                   
BSCALE  =   1.0000000000000000 /physical = BZERO + BSCALE*array_value           
BZERO   =   32768.000000000000 /physical = BZERO + BSCALE*array_value           

Here's a link to download the full file

As a workaround for this one file, I can use ffgidt. Is this a bug in cfitsio?

Trying to compile a crate with fitsio="0.17.0" as a dependency on a Raspberry Pi running Raspberry Pi OS Lite. This is the error message:

error: no rules expected the token `DataType`
   --> /root/.cargo/registry/src/github.com-1285ae84e5963aae/fitsio-0.17.0/src/images.rs:295:42
    |
91  | macro_rules! read_image_impl_vec {
    | -------------------------------- when calling this macro
...
295 | read_image_impl_vec!(i64, i64::default() DataType::TLONGLONG);
    |                                         -^^^^^^^^ no rules expected this token in macro call
    |                                         |
    |                                         help: missing comma here

error: no rules expected the token `DataType`
   --> /root/.cargo/registry/src/github.com-1285ae84e5963aae/fitsio-0.17.0/src/images.rs:308:39
    |
210 | macro_rules! write_image_impl {
    | ----------------------------- when calling this macro
...
308 | write_image_impl!(i64, i64::default() DataType::TLONGLONG);
    |                                      -^^^^^^^^ no rules expected this token in macro call
    |                                      |
    |                                      help: missing comma here

error[E0425]: cannot find function `fits_read_key_lnglng` in this scope
   --> /root/.cargo/registry/src/github.com-1285ae84e5963aae/fitsio-0.17.0/src/headers.rs:61:22
    |
61  |   reads_key_impl!(i64, fits_read_key_lnglng);
    |                        ^^^^^^^^^^^^^^^^^^^^ help: a function with a similar name exists: `fits_read_key_lng`
    |
   ::: /root/.cargo/registry/src/github.com-1285ae84e5963aae/fitsio-0.17.0/src/longnam.rs:240:1
    |
240 | / pub(crate) unsafe fn fits_read_key_lng(
241 | |     fptr: *mut fitsfile,
242 | |     keyname: *const c_char,
243 | |     value: *mut c_long,
...   |
247 | |     ffgkyj(fptr, keyname, value, comm, status)
248 | | }
    | |_- similarly named function `fits_read_key_lng` defined here

error[E0425]: cannot find function `fits_read_col_lnglng` in this scope
   --> /root/.cargo/registry/src/github.com-1285ae84e5963aae/fitsio-0.17.0/src/tables.rs:156:22
    |
156 |   reads_col_impl!(i64, fits_read_col_lnglng, 0);
    |                        ^^^^^^^^^^^^^^^^^^^^ help: a function with a similar name exists: `fits_read_col_lng`
    |
   ::: /root/.cargo/registry/src/github.com-1285ae84e5963aae/fitsio-0.17.0/src/longnam.rs:198:1
    |
198 | / pub(crate) unsafe fn fits_read_col_lng(
199 | |     fptr: *mut fitsfile,
200 | |     colnum: c_int,
201 | |     firstrow: LONGLONG,
...   |
211 | |     )
212 | | }
    | |_- similarly named function `fits_read_col_lng` defined here

For more information about this error, try `rustc --explain E0425`.

Hi,

Sorry, if I am making an obvious mistake as I am a total rust beginner.

Everything seems to be working fine until I want to create an ndarray from the image in the FITS file.

No matter how I write it, I always get an

the trait bound ndarray::ArrayBase<ndarray::OwnedRepr<u32>, ndarray::dimension::dim::Dim<ndarray::dimension::dynindeximpl::IxDynImpl>>: fitsio::images::ReadImage is not satisfied

error.

I think this is not just caused by my code as I can reproduce it by trying to compile the example code in this repo:

➜  ~/tmp git clone [email protected]:mindriot101/rust-fitsio.git
Klone nach 'rust-fitsio' ...
remote: Enumerating objects: 121, done.
remote: Counting objects: 100% (121/121), done.
remote: Compressing objects: 100% (70/70), done.
remote: Total 5665 (delta 65), reused 88 (delta 46), pack-reused 5544
Empfange Objekte: 100% (5665/5665), 6.85 MiB | 2.05 MiB/s, Fertig.
Löse Unterschiede auf: 100% (4305/4305), Fertig.
➜  ~/tmp cd rust-fitsio/homepage/fitsioexample 
➜  ~/…/homepage/fitsioexample git:(master) cargo run --bin ndarray_support
    Updating git repository `https://github.com/mindriot101/rust-fitsio`
    Updating crates.io index
   Compiling num-traits v0.2.6
   Compiling matrixmultiply v0.1.15
   Compiling libc v0.2.51
   Compiling pkg-config v0.3.14
   Compiling either v1.5.1
   Compiling num-complex v0.2.1
   Compiling rawpointer v0.1.0
   Compiling ndarray v0.11.2
   Compiling ndarray v0.12.1
   Compiling itertools v0.7.11
   Compiling fitsio-sys v0.3.0 (https://github.com/mindriot101/rust-fitsio#98910ee3)
   Compiling num-traits v0.1.43
   Compiling num-complex v0.1.43
   Compiling fitsio v0.14.1 (https://github.com/mindriot101/rust-fitsio#98910ee3)
   Compiling fitsioexample v0.1.0 (/home/lukas/tmp/rust-fitsio/homepage/fitsioexample)
error[E0277]: the trait bound `ndarray::ArrayBase<ndarray::OwnedRepr<f32>, ndarray::Dim<ndarray::IxDynImpl>>: fitsio::images::ReadImage` is not satisfied
  --> src/bin/ndarray_support.rs:12:31
   |
12 | let image: ArrayD<f32> = phdu.read_image(&mut fptr)?;
   |                               ^^^^^^^^^^ the trait `fitsio::images::ReadImage` is not implemented for `ndarray::ArrayBase<ndarray::OwnedRepr<f32>, ndarray::Dim<ndarray::IxDynImpl>>`

error: aborting due to previous error

For more information about this error, try `rustc --explain E0277`.
error: Could not compile `fitsioexample`.

To learn more, run the command again with --verbose.

Maybe it isn't working because I seem to be using the latest rust version:

➜ cargo --version
cargo 1.33.0 (f099fe94b 2019-02-12)
➜ rustc --version
rustc 1.33.0 (2aa4c46cf 2019-02-28)

Trying to read FITS file with RGB image

use fitsio::{*, images::*, hdu::*};

fn main() {
    let mut fptr = FitsFile::open("some_color_fits.fit").unwrap();
    let image_hdu = fptr.primary_hdu().unwrap();

    if let HduInfo::ImageInfo { shape, .. } = &image_hdu.info {
        assert!(shape.len() == 3 && shape[0] == 3, "Is not RGB image");

        let height = shape[1];
        let width = shape[2];

        let red_data: Vec<f32> = image_hdu.read_rows(&mut fptr, 0, width*height).unwrap(); // <- Panic here
        let green_data: Vec<f32> = image_hdu.read_rows(&mut fptr, width*height, width*height).unwrap();
        let blue_data: Vec<f32> = image_hdu.read_rows(&mut fptr, 2*width*height, width*height).unwrap();
    }
}

FIT file example: https://drive.google.com/file/d/1g7MW2_rEF8DhIYOUITIqEa_kPH3faLFO/view (not mine. its link from cloudynights.com)

Hi @mindriot101, me again. The first commit here should help keep dependabot quiet. It was my mistake to pull libc down to 0.1.*; it should've always been something in 0.2.*.

The second commit also pins us against the most-current version of ndarray. In the main branch, the >=0.8.0 range is not very different from what it used to be (0), but this commit solves an important problem; if a new version of ndarray (e.g. 0.16.0) is released and a crate is using both rust-fitsio and ndarray 0.15.*, cargo will eagerly use ndarray 0.16.0 for rust-fitsio and 0.15.* otherwise, causing interoperability issues. This has caused me great pain in the past (not via rust-fitsio, mind you) but I've only relatively recently understood why.

Anyway, let me know what you think! Cheers.

Updates the requirements on bindgen to permit the latest version.

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

We should add coverage for the individual features. This could be done via a matrix of features that we test, then combining the coverage via the coveralls action finaliser. This way we have more accurate coverage for branches that are not taken.